TY - JOUR AU - Macklin, D. N. AU - Ruggero, N. A. AU - Covert, M. W. PY - 2014 DA - 2014// TI - The future of whole-cell modeling JO - Curr Opin Biotechnol VL - 28 UR - https://doi.org/10.1016/j.copbio.2014.01.012 DO - 10.1016/j.copbio.2014.01.012 ID - Macklin2014 ER - TY - JOUR AU - Karr, J. R. AU - Sanghvi, J. C. AU - Macklin, D. N. AU - Gutschow, M. V. AU - Jacobs, J. M. AU - Bolival Jr, B. AU - Assad-Garcia, N. AU - Glass, J. I. AU - Covert, M. W. PY - 2012 DA - 2012// TI - A whole-cell computational model predicts phenotype from genotype JO - Cell VL - 150 UR - https://doi.org/10.1016/j.cell.2012.05.044 DO - 10.1016/j.cell.2012.05.044 ID - Karr2012 ER - TY - JOUR AU - Michael, D. G. AU - Maier, E. J. AU - Brown, H. AU - Gish, S. R. AU - Fiore, C. AU - Brown, R. H. AU - Brent, M. R. PY - 2016 DA - 2016// TI - Model-based transcriptome engineering promotes a fermentative transcriptional state in yeast JO - Proc Natl Acad Sci VL - 113 UR - https://doi.org/10.1073/pnas.1603577113 DO - 10.1073/pnas.1603577113 ID - Michael2016 ER - TY - JOUR AU - Gatto, F. AU - Miess, H. AU - Schulze, A. AU - Nielsen, J. PY - 2015 DA - 2015// TI - Flux balance analysis predicts essential genes in clear cell renal cell carcinoma metabolism JO - Sci Rep VL - 5 UR - https://doi.org/10.1038/srep10738 DO - 10.1038/srep10738 ID - Gatto2015 ER - TY - JOUR AU - Steuer, R. PY - 2007 DA - 2007// TI - Computational approaches to the topology, stability and dynamics of metabolic networks JO - Phytochemistry VL - 68 UR - https://doi.org/10.1016/j.phytochem.2007.04.041 DO - 10.1016/j.phytochem.2007.04.041 ID - Steuer2007 ER - TY - BOOK PY - 2006 DA - 2006// TI - The Regulatory Genome PB - Academic Press CY - Burlington ID - ref6 ER - TY - JOUR AU - Lewis, N. E. AU - Hixson, K. K. AU - Conrad, T. M. AU - Lerman, J. A. AU - Charusanti, P. AU - Polpitiya, A. D. AU - Adkins, J. N. AU - Schramm, G. AU - Purvine, S. O. AU - Lopez-Ferrer, D. PY - 2010 DA - 2010// TI - Omic data from evolved e. coli are consistent with computed optimal growth from genome-scale models JO - Mol Syst Biol VL - 6 ID - Lewis2010 ER - TY - JOUR AU - Colijn, C. AU - Brandes, A. AU - Zucker, J. AU - Lun, D. S. AU - Weiner, B. AU - Farhat, M. R. AU - Cheng, T. Y. AU - Moody, D. B. AU - Murray, M. AU - Galagan, J. E. PY - 2009 DA - 2009// TI - Interpreting expression data with metabolic flux models: predicting mycobacterium tuberculosis mycolic acid production JO - PLoS Comput Biol VL - 5 UR - https://doi.org/10.1371/journal.pcbi.1000489 DO - 10.1371/journal.pcbi.1000489 ID - Colijn2009 ER - TY - JOUR AU - Becker, S. A. AU - Palsson, B. O. PY - 2008 DA - 2008// TI - Context-specific metabolic networks are consistent with experiments JO - PLoS Comput Biol VL - 4 UR - https://doi.org/10.1371/journal.pcbi.1000082 DO - 10.1371/journal.pcbi.1000082 ID - Becker2008 ER - TY - JOUR AU - Covert, M. W. AU - Xiao, N. AU - Chen, T. J. AU - Karr, J. R. PY - 2008 DA - 2008// TI - Integrating metabolic, transcriptional regulatory and signal transduction models in escherichia coli JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn352 DO - 10.1093/bioinformatics/btn352 ID - Covert2008 ER - TY - JOUR AU - Chandrasekaran, S. AU - Price, N. D. PY - 2010 DA - 2010// TI - Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in escherichia coli and mycobacterium tuberculosis JO - Proc Natl Acad Sci VL - 107 UR - https://doi.org/10.1073/pnas.1005139107 DO - 10.1073/pnas.1005139107 ID - Chandrasekaran2010 ER - TY - JOUR AU - Motamedian, E. AU - Mohammadi, M. AU - Shojaosadati, S. A. AU - Heydari, M. PY - 2017 DA - 2017// TI - Trfba: an algorithm to integrate genome-scale metabolic and transcriptional regulatory networks with incorporation of expression data JO - Bioinformatics VL - 33 ID - Motamedian2017 ER - TY - JOUR AU - Elati, M. AU - Neuvial, P. AU - Bolotin-Fukuhara, M. AU - Barillot, E. AU - Radvanyi, F. AU - Rouveirol, C. PY - 2007 DA - 2007// TI - Licorn: learning cooperative regulation networks from gene expression data JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm352 DO - 10.1093/bioinformatics/btm352 ID - Elati2007 ER - TY - JOUR AU - Nicolle, R. AU - Radvanyi, F. AU - Elati, M. PY - 2015 DA - 2015// TI - Coregnet: reconstruction and integrated analysis of co-regulatory networks JO - Bioinformatics VL - 31 UR - https://doi.org/10.1093/bioinformatics/btv305 DO - 10.1093/bioinformatics/btv305 ID - Nicolle2015 ER - TY - JOUR AU - Marbach, D. AU - Costello, J. C. AU - Küffner, R. AU - Vega, N. M. AU - Prill, R. J. AU - Camacho, D. M. AU - Allison, K. R. AU - Kellis, M. AU - Collins, J. J. AU - Stolovitzky, G. PY - 2012 DA - 2012// TI - Wisdom of crowds for robust gene network inference JO - Nat Methods VL - 9 UR - https://doi.org/10.1038/nmeth.2016 DO - 10.1038/nmeth.2016 ID - Marbach2012 ER - TY - JOUR AU - Österlund, T. AU - Nookaew, I. AU - Bordel, S. AU - Nielsen, J. PY - 2013 DA - 2013// TI - Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling JO - BMC Syst Biol VL - 7 UR - https://doi.org/10.1186/1752-0509-7-36 DO - 10.1186/1752-0509-7-36 ID - Österlund2013 ER - TY - JOUR AU - Machado, D. AU - Herrgård, M. PY - 2014 DA - 2014// TI - Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism JO - PLoS Comput Biol VL - 10 UR - https://doi.org/10.1371/journal.pcbi.1003580 DO - 10.1371/journal.pcbi.1003580 ID - Machado2014 ER - TY - JOUR AU - Chebil, I. AU - Nicolle, R. AU - Santini, G. AU - Rouveirol, C. AU - Elati, M. PY - 2014 DA - 2014// TI - Hybrid method inference for the construction of cooperative regulatory network in human JO - NanoBioscience IEEE Trans VL - 13 UR - https://doi.org/10.1109/TNB.2014.2316920 DO - 10.1109/TNB.2014.2316920 ID - Chebil2014 ER - TY - JOUR AU - Faith, J. J. AU - Driscoll, M. E. AU - Fusaro, V. A. AU - Cosgrove, E. J. AU - Hayete, B. AU - Juhn, F. S. AU - Schneider, S. J. AU - Gardner, T. S. PY - 2008 DA - 2008// TI - Many microbe microarrays database: uniformly normalized affymetrix compendia with structured experimental metadata JO - Nucleic Acids Res VL - 36 ID - Faith2008 ER - TY - JOUR AU - Teixeira, M. C. AU - Monteiro, P. AU - Jain, P. AU - Tenreiro, S. AU - Fernandes, A. R. AU - Mira, N. P. AU - Alenquer, M. AU - Freitas, A. T. AU - Oliveira, A. L. AU - Sá-Correia, I. PY - 2006 DA - 2006// TI - The yeastract database: a tool for the analysis of transcription regulatory associations in saccharomyces cerevisiae JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkj013 DO - 10.1093/nar/gkj013 ID - Teixeira2006 ER - TY - JOUR AU - Stark, C. AU - Breitkreutz, B. J. AU - Reguly, T. AU - Boucher, L. AU - Breitkreutz, A. AU - Tyers, M. PY - 2006 DA - 2006// TI - Biogrid: a general repository for interaction datasets JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkj109 DO - 10.1093/nar/gkj109 ID - Stark2006 ER - TY - CHAP AU - Nicolle, R. AU - Elati, M. AU - Radvanyi, F. PY - 2012 DA - 2012// TI - Network transformation of gene expression for feature extraction BT - 2012 11th International Conference on Machine Learning and Applications PB - IEEE CY - Piscataway ID - Nicolle2012 ER - TY - JOUR AU - Breitkreutz, A. AU - Choi, H. AU - Sharom, J. R. AU - Boucher, L. AU - Neduva, V. AU - Larsen, B. AU - Lin, Z. Y. AU - Breitkreutz, B. J. AU - Stark, C. AU - Liu, G. PY - 2010 DA - 2010// TI - A global protein kinase and phosphatase interaction network in yeast JO - Science VL - 328 UR - https://doi.org/10.1126/science.1176495 DO - 10.1126/science.1176495 ID - Breitkreutz2010 ER - TY - JOUR AU - Rintala, E. AU - Toivari, M. AU - Pitkänen, J. P. AU - Wiebe, M. G. AU - Ruohonen, L. AU - Penttilä, M. PY - 2009 DA - 2009// TI - Low oxygen levels as a trigger for enhancement of respiratory metabolism in saccharomyces cerevisiae JO - BMC Genomics VL - 10 UR - https://doi.org/10.1186/1471-2164-10-461 DO - 10.1186/1471-2164-10-461 ID - Rintala2009 ER - TY - JOUR AU - Orth, J. D. AU - Thiele, I. AU - Palsson, B. PY - 2010 DA - 2010// TI - What is flux balance analysis? JO - Nat Biotechnol VL - 28 UR - https://doi.org/10.1038/nbt.1614 DO - 10.1038/nbt.1614 ID - Orth2010 ER - TY - JOUR AU - Jensen, P. A. AU - Lutz, K. A. AU - Papin, J. A. PY - 2011 DA - 2011// TI - Tiger: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks JO - BMC Syst Biol VL - 5 UR - https://doi.org/10.1186/1752-0509-5-147 DO - 10.1186/1752-0509-5-147 ID - Jensen2011 ER - TY - STD TI - Osorio D, Botero K, Gonzalez J, Pinzon A. exp2flux: Convert Gene EXPression Data to FBA FLUXes. 2016. http://CRAN.R-project.org/package=exp2flux. R package version 0.1. Accessed Feb 2017. UR - http://CRAN.R-project.org/package=exp2flux ID - ref27 ER - TY - STD TI - Dugas C, Bengio Y, Bélisle F, Nadeau C, Garcia R. Incorporating second-order functional knowledge for better option pricing. Adv Neural Inf Process Syst. 2001;:472–8. ID - ref28 ER - TY - STD TI - Gelius-Dietrich G, Fritzemeier CJ, Desouki AA, Lercher MJ. sybil – efficient constraint-based modelling in r. BMC Syst Biol. 2013; 7(1):125. doi:10.1186/1752-0509-7-125. http://www.biomedcentral.com/1752-0509/7/125. UR - http://www.biomedcentral.com/1752-0509/7/125 ID - ref29 ER - TY - CHAP AU - Močkus, J. ED - Marchuk, G. I. PY - 1975 DA - 1975// TI - On bayesian methods for seeking the extremum BT - Optimization Techniques IFIP Technical Conference Novosibirsk, July 1-7, 1974 PB - Springer Berlin Heidelberg CY - Berlin ID - Močkus1975 ER - TY - STD TI - Yan Y. rBayesianOptimization: Bayesian Optimization of Hyperparameters. http://github.com/yanyachen/rBayesianOptimization. R package version 1.1.0. Accessed Feb 2017. UR - http://github.com/yanyachen/rBayesianOptimization ID - ref31 ER - TY - JOUR AU - Brauer, M. J. AU - Saldanha, A. J. AU - Dolinski, K. AU - Botstein, D. PY - 2005 DA - 2005// TI - Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures JO - Mol Biol Cell VL - 16 UR - https://doi.org/10.1091/mbc.E04-11-0968 DO - 10.1091/mbc.E04-11-0968 ID - Brauer2005 ER - TY - JOUR AU - DeRisi, J. L. AU - Iyer, V. R. AU - Brown, P. O. PY - 1997 DA - 1997// TI - Exploring the metabolic and genetic control of gene expression on a genomic scale JO - Science VL - 278 UR - https://doi.org/10.1126/science.278.5338.680 DO - 10.1126/science.278.5338.680 ID - DeRisi1997 ER - TY - JOUR AU - Zampar, G. G. AU - Kümmel, A. AU - Ewald, J. AU - Jol, S. AU - Niebel, B. AU - Picotti, P. AU - Aebersold, R. AU - Sauer, U. AU - Zamboni, N. AU - Heinemann, M. PY - 2013 DA - 2013// TI - Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast JO - Mol Syst Biol VL - 9 UR - https://doi.org/10.1038/msb.2013.11 DO - 10.1038/msb.2013.11 ID - Zampar2013 ER - TY - JOUR AU - de Jong, B. W. AU - Siewers, V. AU - Nielsen, J. PY - 2016 DA - 2016// TI - Physiological and transcriptional characterization of saccharomyces cerevisiae engineered for production of fatty acid ethyl esters JO - FEMS Yeast Res VL - 16 UR - https://doi.org/10.1093/femsyr/fov105 DO - 10.1093/femsyr/fov105 ID - de Jong2016 ER - TY - JOUR AU - Varma, A. AU - Palsson, B. O. PY - 1994 DA - 1994// TI - Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type escherichia coli w3110 JO - Appl Environ Microbiol VL - 60 ID - Varma1994 ER - TY - JOUR AU - Segrè, D. AU - Zucker, J. AU - Katz, J. AU - Lin, X. AU - D’haeseleer, P. AU - Rindone, W. P. AU - Kharchenko, P. AU - Nguyen, D. H. AU - Wright, M. A. AU - Church, G. M. PY - 2003 DA - 2003// TI - From annotated genomes to metabolic flux models and kinetic parameter fitting JO - OMICS A J Integrative Biol VL - 7 UR - https://doi.org/10.1089/153623103322452413 DO - 10.1089/153623103322452413 ID - Segrè2003 ER - TY - JOUR AU - Liao, J. C. AU - Boscolo, R. AU - Yang, Y. L. AU - Tran, L. M. AU - Sabatti, C. AU - Roychowdhury, V. P. PY - 2003 DA - 2003// TI - Network component analysis: reconstruction of regulatory signals in biological systems JO - Proc Natl Acad Sci VL - 100 UR - https://doi.org/10.1073/pnas.2136632100 DO - 10.1073/pnas.2136632100 ID - Liao2003 ER - TY - JOUR AU - Kochanowski, K. AU - Gerosa, L. AU - Brunner, S. F. AU - Christodoulou, D. AU - Nikolaev, Y. V. AU - Sauer, U. PY - 2017 DA - 2017// TI - Few regulatory metabolites coordinate expression of central metabolic genes in escherichia coli JO - Mol Syst Biol VL - 13 UR - https://doi.org/10.15252/msb.20167402 DO - 10.15252/msb.20167402 ID - Kochanowski2017 ER -